|
|
Nextflow |
12 |
Nextflow pipeline for Mutect2 somatic variant calling best practices |
Jul 14, 2022 |
|
|
Nextflow |
7 |
Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices |
Dec 11, 2021 |
|
|
None |
2 |
Variant-Calling-Example |
Apr 20, 2023 |
|
|
Shell |
4 |
H3A variant calling pipeline |
Apr 20, 2021 |
|
|
Cython |
8 |
TIDDIT - structural variant calling |
Jun 03, 2022 |
|
|
Python |
2 |
variant calling and processing |
Apr 27, 2022 |
|
|
Cython |
52 |
TIDDIT - structural variant calling |
Mar 26, 2023 |
|
|
R |
6 |
Tumor-only variant calling |
May 17, 2023 |
|
|
Python |
29 |
10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling |
Feb 15, 2023 |
|
|
Nextflow |
30 |
Deep Variant as a Nextflow pipeline |
Jan 06, 2022 |
|
|
Jupyter Notebook |
4 |
A bioinformatic variant calling pipeline |
Aug 24, 2017 |
|
|
Nextflow |
9 |
gatk4 RNA variant calling pipeline |
Aug 02, 2022 |
|
|
Python |
46 |
Benchmarking toolkit for variant calling |
Mar 08, 2023 |
|
|
Shell |
2 |
Variant calling and PSMC workflows |
Oct 22, 2023 |
|
|
Nextflow |
3 |
Nextflow pipeline for CNV calling with PURPLE |
Jun 24, 2023 |
|
|
Nextflow |
3 |
This is a nextflow pipeline for variant calling of low frequency variants in panel/WES high-throughput … |
Mar 23, 2022 |
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|
None |
22 |
Nextflow + Docker tutorial material |
Jan 13, 2023 |
|
|
Nextflow |
7 |
Small variant calling for human samples |
Jul 30, 2022 |
|
|
C |
10 |
TOPMed Freeze 3 variant calling pipeline |
Nov 24, 2021 |
|
|
None |
2 |
Consensus assembly and variant calling workflow |
Aug 17, 2017 |
|
|
Groovy |
2 |
Small variant calling for haploid samples |
Apr 25, 2022 |
|
|
None |
15 |
Minor Variant Calling and Phasing Tools |
Jul 31, 2022 |
|
|
Shell |
20 |
Variant Calling Pipeline in Cromwell/WDL |
Nov 13, 2020 |
|
|
C++ |
21 |
Interface to various variant calling formats. |
Apr 19, 2022 |
|
|
None |
12 |
Consensus assembly and variant calling workflow. |
Oct 27, 2022 |
|
|
Nextflow |
2 |
A nextflow pipeline for calling and annotating variants |
Oct 24, 2023 |
|
|
Scala |
3 |
Tools for comparing somatic variant calling tools. |
May 20, 2021 |
|
|
None |
5 |
SNP and variant calling pipeline for bacteria |
Feb 02, 2023 |
|
|
Python |
3 |
Snakemake pipeline for variant calling using GATK |
Mar 02, 2023 |
|
|
Python |
2 |
Validate prioritization of tumor-only variant calling |
Jun 04, 2016 |
|
|
Groovy |
2 |
NextFlow framework to streamline the Genalice variant call pipeline |
Dec 12, 2016 |
|
|
Shell |
3 |
Nextflow pipeline for standardised variant calls on canine genomes |
Nov 11, 2020 |
|
|
Nextflow |
33 |
Nextflow basic tutorial for newbie users |
Mar 06, 2023 |
|
|
Nextflow |
74 |
Nextflow training material for introductory tutorial |
Apr 10, 2023 |
|
|
Nextflow |
3 |
Nextflow based pipeline for Zika tutorial |
Dec 15, 2021 |
|
|
Python |
5 |
Andersen Lab Python-based pipeline for variant calling. |
Jan 28, 2023 |
|
|
C++ |
29 |
Genomes on the Cloud, Mapping & Variant Calling Pipelines |
Jul 29, 2022 |
|
|
R |
2 |
Example variant calling workflow using R targets package |
Jan 31, 2023 |
|
|
Python |
60 |
Variant calling tool for long-read sequencing data |
May 02, 2023 |
|
|
Python |
2 |
Genomic Pipelines (Mapping + Variant Calling) from NGS Data |
Mar 08, 2021 |
|
|
Nextflow |
3 |
Variant calling pipeline for the Illumina Dragen platform |
Apr 17, 2023 |
|
|
Python |
2 |
Snakemake pipeline for read mapping and variant calling |
Sep 08, 2022 |
|
|
R |
5 |
Automated Pipeline for Variant/Haplotype Calling and Filtering |
May 13, 2023 |
|
|
Shell |
5 |
A Nextflow variant normalization pipeline based on vt and bcftools |
Nov 22, 2021 |
|
|
Python |
71 |
pbsv - PacBio structural variant (SV) calling and analysis tools |
Jul 14, 2022 |
|
|
Scala |
3 |
GATK QScripts used in our illumina variant calling pipeline. |
Jul 22, 2016 |
|
|
Jupyter Notebook |
22 |
SARS-CoV-2 variant calling and consensus assembly pipeline |
Apr 28, 2023 |
|
|
Python |
3 |
Multisample DNAseq variant calling pipeline for use in diagnostics |
Mar 11, 2021 |
|
|
wdl |
6 |
WDL workflows for variant calling and assembly using ONT |
Apr 19, 2023 |
|
|
R |
2 |
Wrapper and analysis scripts for RNA variant calling pipeline |
Nov 19, 2023 |